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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4f9b

2.500 Å

X-ray

2012-05-18

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cell division cycle 7-related protein kinase
ID:CDC7_HUMAN
AC:O00311
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.7.11.1


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:46.032
Number of residues:24
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.723698.625

% Hydrophobic% Polar
48.7951.21
According to VolSite

Ligand :
4f9b_2 Structure
HET Code: 0SY
Formula: C12H11N3O
Molecular weight: 213.235 g/mol
DrugBank ID: -
Buried Surface Area:66.03 %
Polar Surface area: 57.78 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
29.1259-13.814329.7251


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
CAECG1VAL- 724.390Hydrophobic
CADCBALA- 883.830Hydrophobic
OAANZLYS- 902.8171.9H-Bond
(Protein Donor)
CADCEMET- 1184.030Hydrophobic
CADSDMET- 1343.950Hydrophobic
NAINLEU- 1373.14177.44H-Bond
(Protein Donor)
CAMCD1LEU- 1843.710Hydrophobic
CADCG1VAL- 1954.210Hydrophobic
NAJOD1ASP- 1962.61160.56H-Bond
(Ligand Donor)